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bioRxiv · 10.1101/2024.01.06.573815

From Understudied to Understood: Multi-Omics Analysis with MiniENCODE Exemplified by Zebrafish

Yang, H.·Shan, Z.·Shang, H.·Jiang, P.·Li, Y.·Tu, Q.
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Abstract

Building multi-omics resources for understudied organisms requires assay selection, public-data curation, gene identifier handling, portal deployment, and visualization, yet these tasks are rarely packaged into a reusable framework. To fill this gap, we developed the mini Omics Data Portal (miniODP), which combines species pages, gene-centric modules, genome browsing, and sequence search with configuration files, species onboarding workflows, and demonstration data for self-deployment. Alongside the software, we propose miniENCODE core assays: a reduced RNA-seq, ATAC-seq, and H3K27ac profiling set for regulatory analysis. Current miniODP includes seven species, covering 3,568 bulk runs, 3.61 million cells, and 1,865 genome-browser tracks. Matched core-assay datasets support regulatory outputs. As a zebrafish benchmark, using datasets from three core assays and 17 samples, we identified 52,350 enhancer-like signatures (ELSs) and constructed ELS-to-gene linkages and gene regulatory networks (GRNs). Genes near H3K27ac-supported ELSs were expressed at higher levels than those near ATAC-only distal peaks. Literature curation of top TFs from zebrafish and cattle GRNs found 19 direct, 15 indirect, and six unsupported cases among 40 candidates. Datasets lacking matched core assays still provide browsing, visualization, and search functions. miniODP serves as a reusable framework for constructing and extending multi-omics resources for understudied organisms. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/573815v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1542265org.highwire.dtl.DTLVardef@9e5424org.highwire.dtl.DTLVardef@a630d5org.highwire.dtl.DTLVardef@d0163c_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Yang, H., Shan, Z., Shang, H., Jiang, P., Li, Y., Tu, Q.. 2024-01-07. From Understudied to Understood: Multi-Omics Analysis with MiniENCODE Exemplified by Zebrafish. https://doi.org/10.1101/2024.01.06.573815

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